Nanopore sequencing systems generally use a protein pore in a planar lipid bilayer (PLB) suspended over a well (e.g., a cylindrical well) containing an electrolyte solution, which is also present in a much larger exterior reservoir (e.g., above the well). A working electrode and counter electrode are used to apply an electrical bias across the well and the exterior reservoir. The PLB extends over the well to both electrically and physically seal the well, and the PLB separates the well from the larger exterior reservoir. While neutral molecules, such as water and dissolved gases, may pass through the PLB, ions may not. A protein pore in the PLB provides a path for ions to be conducted into and out of the well.
Protein pores such as alpha hemolysin (aHL) are known to preferentially conduct either anions or cations and to have unequal conductivity under positive and negative electrical bias (Noskov et al., (2004) Biophys J. 87:2299). Such properties may lead to a net influx from or efflux into the well, which leads to diffusion of water through the PLB to balance the electrolyte concentration between the well and the external reservoir. Such diffusion can cause instability.